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Background  Ionic liquids (ILs) are a promising alternative for organic solvents because these liquids exhibit unique properties and enhanced steroid 1-dehydrogenation biotransformation caused by  Arthrobacter simplex  CPCC 140451 ( ASP ). However, the effect of ILs on the whole cell itself remains poorly understood and must be further investigated.    Results  A comparative investigation was performed to determine the effect of imidazolium-based ILs, namely, hydrophobic [PrMIm]PF 6 , and hydrophilic [PrMIm]BF 4 , on the steroid conversion, activity, permeability, and material basis of  ASP  cells. Both ILs weakened permeability barriers, enhanced steroid transformation, whereas reduced the activity of cells. The influence of [PrMIm]PF 6  on the steroid conversion, permeability and activity of cells is more serious than that of [PrMIm]BF 4  Transmission electron microscopy micrographs directly showed wrinkles, gross creases, and several small pores in ILs-treated cells surface. The total lipid content of [PrMIm]BF 4 -treated cells reduced by 8.3 %, while that of [PrMIm]PF 6 -treated cells reduced twice more, among which the content of long-chain fatty acids was decreased, whereas the content of unsaturated fatty acids was increased. The protein profile of LC–MS/MS revealed that the reduced proteins of cells treated with the two ILs were mainly located in the cytoplasm and plasma membrane, 19.27 % of reduced proteins were located on the cell membrane for [PrMIm]PF 6 -pretreated cells, whereas only 12.8 % for [PrMIm]BF 4 -pretreated cells. It suggests that most reduced proteins functioned in energy production and conversion, material transport and metabolism, signal recognition and transmission, transcription, and translation and posttranslational modification. In particular, the identified differential proteins functioned in the pentose phosphate pathway, synthesis of purines and pyrimidines, and oxidative phosphorylation and fatty acid pathway.    Conclusion  Treatment with ILs improved permeability at the molecular level and exerted significant positive effects on steroid conversion. This study provides a material basis and elucidates the mechanisms underlying cellular changes that enhanced conversion rate.    Electronic supplementary material  The online version of this article (doi:10.1186/s12934-016-0518-3) contains supplementary material, which is available to authorized users.

Effects of two kinds of imidazolium-based ionic liquids on the characteristics of steroid-transformation Arthrobacter simplex